your restraint weight is very weak.
it will calculate the non-fit rmsd for atoms in
the rmsmask, but will do no best fit.
when you use ptraj and do an alignment, then
you already have something different from what
you asked sander to do. try to use ptraj to calculate
the rmsd without any fitting at all.
alternatively, use a much stronger restraint
weight and see if the agreement in rmsd improves.
it could be something else, but I am guessing it
is the extremely weak restraint in sander as compared
to actual alignment in ptraj.